EP1409497B1 - Method for preparation of lna phosphoramidites - Google Patents

Method for preparation of lna phosphoramidites Download PDF

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Publication number
EP1409497B1
EP1409497B1 EP02764561A EP02764561A EP1409497B1 EP 1409497 B1 EP1409497 B1 EP 1409497B1 EP 02764561 A EP02764561 A EP 02764561A EP 02764561 A EP02764561 A EP 02764561A EP 1409497 B1 EP1409497 B1 EP 1409497B1
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Prior art keywords
lna
cyanoethyl
ribo
phosphoramidite
tetraisopropylphosphoramidite
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EP02764561A
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German (de)
English (en)
French (fr)
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EP1409497A2 (en
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Troels Koch
Christoph Rosenbohm
Daniel Sejer Pedersen
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Roche Innovation Center Copenhagen AS
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Santaris Pharma AS
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H1/00—Processes for the preparation of sugar derivatives
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H1/00—Processes for the preparation of sugar derivatives
    • C07H1/02—Phosphorylation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals

Definitions

  • the present invention relates to a high yielding, fast method for large-scale LNA phosphoramidites synthesis.
  • LNA Locked Nucleic Acid
  • Oligonucleotide synthesis is typically performed using the phosphoramidite method, invented by Caruthers, U54415732, in 1980 and improved a couple of years later by Köster US4725677.
  • LNA oligomers are being synthesised according to the phosphoramidite method, but so far the large scale supply of LNA monomers has been a problem due to slow reactions, side product formation during the reaction and reagents unstable at room temperature have been employed.
  • tetrazole The mechanism of phosphoramidite activation and coupling in oligonucleotide syntheses has been studied in detail. Traditionally tetrazole has been used (Dahl et al. 1987, Nucleic Acid Research, 15, 1729-1743; Beaucage & Iver, 1992, Tetrahedron, 48, 2223-2311). The proposed mechanism of tetrazole is two step, first tetrazole protonates trivalent phosphorous followed by displacement of the N,N -diisopropylamine by the tetrazolide. This latter intermediate is very reactive with hydroxynucleophiles such as 5'-OH on nucleic acids. Therefore, tetrazole acts both as acid and as nucleophilic agent.
  • Vargeese et al. (Vargeese, C.; Carter, J.; Krivjansky, S.; Settle, A.; Kropp, E.; Peterson, K.; Pieken, W. Nucleic Acid Research, 1998, 26, 1046-1050; WO9816540;) have described an activator for the coupling of phosphoramidites to the 5'-hydroxyl group during oligonucleotide synthesis.
  • the activator is 4,5-dicyanoimidazole (DCI) and its effectiveness is thought to be based on its nucleophilicity. It was shown that DCI significantly increased the yield in phosphoramidite oligomerisation.
  • Vargeese et al. has described a method of small scale DNA phosphoramidite thymine monomer synthesis using DCI, but the method they used provided a moderate yield (75%) after several re-precipitations of the amidite.
  • Kittaka et al. Korean T.; Amano M.; Tanaka H.; Miyasaka T.; Hirose K.; Yoshida T.; Sarai A.; Yasukawa T. and Ishii S. Nucleosides & Nucleotides 18, 2769-2783, 1999
  • Kittaka et al. Korean T.; Amano M.; Tanaka H.; Miyasaka T.; Hirose K.; Yoshida T.; Sarai A.; Yasukawa T. and Ishii S. Nucleosides & Nucleotides 18, 2769-2783, 1999
  • Kittaka et al. Korean T.; Amano M.; Tanaka H.; Mi
  • the present invention provides a novel high yielding and fast method for the large scale synthesis of pure LNA phosphoramidites.
  • the phosphitylation step is crucial. If necessary also a facile and efficient purification is desired, due to the reactivity of the phosphoramidites, so as to avoid their decomposition during purification.
  • An absolute purity of the amidites is a prerequisite because the monomers are used in long sequential oligomerisations over some time where also impurities can cause the decomposition of the phosphoramidites.
  • the present invention provides a method for the synthesis of an LNA phosphoramidite, the method comprising phosphitylation of the 3'-OH groups of an LNA monomer with a 2-cyanoethyl- N , N , N' , N '-tetra-substituted phosphoramidite in the presence of a nucleophilic activator.
  • LNA monomer refers to a ribonucleotide having a 2',4'-bridge (in particular a -O-CH 2 - (oxy-LNA), -S-CH 2 - (thio-LNA), -NR-CH 2 - (amino-LNA, R being hydrogen, C 1-6 -alkyl, phenyl, benzyl, etc.) bridge) as described in the International Patent Application WO9914226 and subsequent WO0056746, WO0056748, WO0066604 and W00228875.
  • LNA monomers of are those referred to as oxy- ⁇ -D-ribo-LNA (cf. Figure 2), thio- ⁇ -D-ribo-LNA, amino- ⁇ -D-ribo-LNA, oxy- ⁇ -L-ribo-LNA (cf. Figure 3), thio- ⁇ -L-ribo-LNA or amino- ⁇ -L-ribo-LNA.
  • LNA phosphoramidite refers to a nucleotide with a protected 5'-hydroxy group (e.g. DMT protected as illustrated in Figures 2 and 3), in which the 3'-hydroxy group is coupled to a trivalent phosphorous atom, which in turn is bonded to a suitable leaving group such as a N,N -dialkylamine, e.g. diisopropylamine and a protecting group such as the cyanoethyl (NCCH 2 CH 2 -) group.
  • a suitable leaving group such as a N,N -dialkylamine, e.g. diisopropylamine and a protecting group such as the cyanoethyl (NCCH 2 CH 2 -) group.
  • Any LNA phosphoramidite that can be used in solid or liquid phase oligonucleotide synthesis can be used in the present invention, including protected dimer and trimer LNA phosphoramidite.
  • 2-cyanoethyl- N,N,N',N' -tetra-substituted phosphoramidite also referred to as "PN 2 -reagent” refers in short to a 2-cyanoethyl- N,N,N',N' -tetra-substituted phosphoramidite, wherein the term “substituted” means a linear, cyclic or branched unsaturated hydrocarbon such as allyl or vinyl or saturated hydrocarbon or substituted hydrocarbon group or aromatic group or substituted aromatic group having 1 to 9 carbon atoms, such as methyl, ethyl, propyl, iso-propyl, pentyl, cyclopentyl, hexyl, cyclohexyl, preferred examples alkyl are methyl, ethyl, propyl, iso-propyl, butyl, tert-butyl, iso-butyl, pentyl
  • the LNA monomer as well as the phosphoramidite LNA monomer may carry any nucleobase in the 1' position.
  • nucleobase covers naturally occurring nucleobases as well as non-naturally occurring nucleobases. It should be clear to the person skilled in the art that various nucleobases which previously have been considered “non-naturally occurring” have subsequently been found in nature. Thus, “nucleobase” includes not only the known purine and pyrimidine heterocycles, but also heterocyclic analogues and tautomers thereof.
  • nucleobases are adenine, guanine, thymine, cytosine, uracil, purine, xanthine, diaminopurine, 8-oxo- N 6 -methyladenine, 7-deazaxanthine, 7-deazaguanine, N 4 ,N 4 -ethanocytosin, N 6 ,N 6 -ethano-2,6-diaminopurine, 5-methylcytosine, 5-( C 3 -C 6 )-alkynylcytosine, 5-fluorouracil, 5-bromouracil, pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridin, isocytosine, isoguanin, inosine, N 6 alylpurines, N 6 -acylpurines, N 6 -benzylpurine, N 6 -halopurine, N 6 -vinylpurine, N 6 -acety
  • vinylpyrimidines N 4 -acetylenic pyrimidines, N 4 -acyl pyrimidines, N 4 -hydroxyalkyl pyrimidines, N 6 -thioalkyl pyrimidines, thymine, cytosine, 6-azapyrimidine, including-6-azacytosine, 2- and/or 4-mercaptopyrimidine, uracil, C 5 -alkylpyrimidines, C 5 -benzylpyrimidines, C 5 -halopyrimidines, C 5 -vinylpyrimidine, C 5 -acetylenic pyrimidine, C 5 -acyl pyrimidine, C 5 -hydroxyalkyl purine, C 5 -amidopyrimidine, C 5 -cyanopyrimidine, C 5 -nitropyrimidine, C 5 -aminopyrimdine, N 2 -alkylpurines, N 2 -alkyl-6-thiopurines, 5-azacy
  • Suitable protecting groups are well known to those skilled in the art, and included trimethylsilyl, dimethylhexylsilyl, t-butyldimenthylsilyl, and t -butyldiphenylsilyl, trityl, alkyl groups, acyl groups such as acetyl and propionyl, methanesulfonyl, and p-toluenesulfonyl, imines such as N-dimethylmethyleneeneamine and dibutylmethyleneeneamine.
  • Preferred bases include cytosine, 5-methylcytosine uracil, thymine, adenine and guanine.
  • LNA phosphoramidites according to the present invention are prepared in high yield with 2-cyanoethyl -N,N,N',N' -tetraisopropylphosphoramidite (a PN 2 -reagent). This reagent has not successfully been used to prepare LNA phosphoramidites before. Previously 2-cyanoethyl- N , N -diisopropylchlorophosphoramidite has been used for preparation of LNA amidites. This has not afforted the high purity, high yields and low reaction times according to the present invention.
  • 2-cyanoethyl -N,N,N',N' -tetraisopropylphosphoramidite can be activated by 4,5-dicyanoimidazole and that this complex provides the accurate reactivity, during the conditions described, to secure efficient phosphitylation of all 4 LNA DMT-protected nucleosides including the G-nucleoside.
  • Another advantage of the present invention is that the reactions are finished in 0.5-4 hours, preferably 1.0-3.5 hours, and that chromatography of the LNA amidites is unnecessary due to the efficient reaction.
  • the phosphitylation reaction is typically allowed to proceed for 0.1-12 hours, such as 0.2-8 hours, e.g. 0.5-4.0 hours, such as 1.0-3.5 hours.
  • an LNA phosphoramidite for direct use in oligonucleotide synthesis may be obtained directly or by simple precipitation of the product from the reaction mixture.
  • the method comprises at the most one precipitation step.
  • Suitable nucleophilic activators for use in the present invention include, but are not limited to, 4,5-dicyanoimidazole (DCI), 4-alkylthioimidazole, 2-alkylthioimidazole, 2-nitroimidazole, 4-nitroimidazole, 4,5-dihaloimidazole, 4-haloimidazole, 2-haloimidazole and 5-alkoxytetrazole.
  • DCI is the preferred nucleophilic activator.
  • DCI has a pK a of 5.2 and is easily dissolved in acetonitrile.
  • Suitable PN 2 -reagents are for example, but not limited to, 2-cyanoethyl- N,N,N',N' -tetraisopropylphosphoramidite and 2-cyanoethyl- N,N,N',N' -tetraethylphosphoramidite and the reagents described by Dahl, B.H., Nielsen J. and Dahl O. Nucleic Acid Research, 1987, 15, 1729-1743 all incorporated here by reference.
  • 2-cyanoethyl- N,N,N',N' -tetraisopropylphosphoramidite and 2-cyanoethyl- N,N,N',N' -tetraethylphosphoramidite are especially relevant, in particular 2-cyanoethyl- N,N,N',N' -tetraisopropylphosphoramidite.
  • a currently preferred combination is where the 2-cyanoethyl-N,N,N',N'-tetra-substituted phosphoramidite is the 2-cyanoethyl- N,N,N',N' -tetraisopropylphosphoramidite and the nucleophilic activator is 4,5-dicyanoimidazole.
  • the molar ratio between the LNA monomer and the nucleophilic activator is typically in the range of 1:0.0001 to 1:10, preferably 1:0.0001 to 1:1, and more preferably 1:0.0001 to 1:0.7.
  • the molar ratio between the LNA monomer and the PN 2 -reagent is typically in the range of 1:0.9 to 1:10, preferably 1:0.95 to 1:5, more preferably 1:1.
  • LNA monomers are those which have a nucleobase selected from guanine, thymine, cytosine, 5-methylcytosine, uracil and adenine, typically in the protected from such as N-benzoyl protected cytosine (C Bz ), N-benzoyl protected methyl cytosine ( Me C Bz ), N-iso-butanoyl protected guanine (G 1bu ), uracil (U), thymine (T), N-benzoyl protected adenine (A Bz ).
  • C Bz N-benzoyl protected cytosine
  • Me C Bz N-benzoyl protected methyl cytosine
  • G 1bu N-iso-butanoyl protected guanine
  • U uracil
  • T thymine
  • a Bz N-benzoyl protected adenine
  • 2-Cyanoethyl- N,N -diisopropylchlorophosphoramidite appeared to have several disadvantages compared to 2-cyanoethyl- N,N,N',N' -tetraisopropylphosphoramidite (PN 2 -reagent). It is unstable at room temperature, expensive and difficult to handle due to its high reactivity. Furthermore undesired reactions with the nudeobases are often observed with 2-cyanoethyl- N,N- diisopropylchlorophosphoramidite ( Figure 1).
  • the compounds 1 , 2 , 4 , 5 and 6 were prepared in a similar manner.

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EP02764561A 2001-07-12 2002-07-12 Method for preparation of lna phosphoramidites Expired - Lifetime EP1409497B1 (en)

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DK200101095 2001-07-12
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JP4402454B2 (ja) 2010-01-20
DE60202681D1 (de) 2005-02-24
WO2003006475A3 (en) 2004-02-26
WO2003006475A2 (en) 2003-01-23
ATE287413T1 (de) 2005-02-15
DK1409497T3 (da) 2005-05-30
AU2002328792A1 (en) 2003-01-29
JP2004536125A (ja) 2004-12-02
DE60202681T2 (de) 2006-01-12

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